Polygenic Score (PGS) ID: PGS003916

Predicted Trait
Reported Trait Arm fat mass (R)
Mapped Trait(s) fat body mass (EFO_0005409)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI23120
Released in PGS Catalog: Nov. 1, 2023
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name INI23120
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 29,790
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000502
Citation (link to publication) Tanigawa Y et al. AJHG (2023)
Ancestry Distribution
Score Development/Training
Multi-ancestry (including European): 100%
  • European
  • South Asian
  • African
  • Additional Diverse Ancestries
319,885 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
Multi-ancestry (excluding European): 20%
  • East Asian
  • Additional Diverse Ancestries
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 319,885 individuals European, South Asian, African unspecified, Other admixed ancestry UKB — — — European, South Asian, African unspecified, Other admixed ancestry —

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM018899 PSS011134|
European Ancestry|
66,604 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Arm fat mass (right) — — R²: 0.14871 [0.14377, 0.15365]
PGS R2 (no covariates): 0.08625 [0.08221, 0.09029]
Incremental R2 (full-covars): 0.08473		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018901 PSS011118|
South Asian Ancestry|
1,457 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Arm fat mass (right) — — R²: 0.19809 [0.1619, 0.23429]
PGS R2 (no covariates): 0.07372 [0.04821, 0.09922]
Incremental R2 (full-covars): 0.04848		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018902 PSS011158|
African Ancestry|
1,169 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Arm fat mass (right) — — R²: 0.13404 [0.09846, 0.16962]
PGS R2 (no covariates): 0.00846 [-0.00178, 0.01869]
Incremental R2 (full-covars): -0.0561		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018903 PSS011178|
Multi-ancestry (excluding European)|
7,840 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Arm fat mass (right) — — R²: 0.14567 [0.13139, 0.15994]
PGS R2 (no covariates): 0.0796 [0.06823, 0.09097]
Incremental R2 (full-covars): 0.06809		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018900 PSS011105|
European Ancestry|
2,837 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Arm fat mass (right) — — R²: 0.12394 [0.1015, 0.14639]
PGS R2 (no covariates): 0.08183 [0.06272, 0.10095]
Incremental R2 (full-covars): 0.083		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS011178 — — 7,840 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011118 — — 1,457 individuals — South Asian — UKB —
PSS011158 — — 1,169 individuals — African unspecified — UKB —
PSS011134 — — 66,604 individuals — European
(white British ancestry)		 — UKB —
PSS011105 — — 2,837 individuals — European
(non-white British ancestry)		 — UKB —